Other amino acids contained in proteins are usually formed by post-translational modification, which is modification after translation in protein synthesis. These modifications are often essential for the function of the protein.

Proline is the only proteinogenic amino acid whose side group is cyclic and links to the a-amino group, forming a secondary amino group. Formerly, proline was misleadingly called an imino acid.

In addition to protein synthesis, amino acids have other biologically-important roles. Glycine and glutamate are neurotransmitters as well as standard amino acids in proteins. Many amino acids are used to synthesize other molecules, for example:

Except for glycine, where R = H, amino acids occur in two possible optical isomers, called D and L. Using the newer Cahn Ingold Prelog priority rules for designating the configuration of optical isomers, the L isomer would assigned the letter S and the D isomer would be assigned the letter R. The L (or S) amino acids represent the vast majority of amino acids found in proteins. D (or R) amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails. They are also abundant components of the cell walls of bacteria.

This information is partially incorrect. L and D isomers are not the same as S and R isomers. S or R isomers may rotate the plane of polarized light to the left or to the right.

Following is a table listing the one letter symbols, the three-letter symbols, and the chemical properties of the side chains of the standard amino acids. The mass listed is the weighted average of all common isotopes, and includes the mass of H2O. The one-letter symbol for an undetermined amino acid is X. The three-letter symbol Asx or one-letter symbol B means the amino acid is either asparagine or aspartic acid, whereas Glx or Z means either glutamic acid or glutamine. The three-letter symbol Sec or one-letter symbol U refers to selenocysteine. The letters J and O are not used.

Very abundant, very versatile. More stiff than glycine, but small enough to pose only small steric limits for the protein conformation. It behaves fairly neutrally, can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside.

The sulfur atom binds readily to heavy metal ions. Under oxidizing conditions, two cysteines can join together by a disulfide bond to form the amino acid cystine. When cystines are part of a protein, insulin for example, this enforces tertiary structure and makes the protein more resistant to unfolding and denaturation; disulphide bridges are therefore common in proteins that have to function in harsh environments, digestive enzymes (e.g., pepsin and chymotrypsin), structural proteins (e.g., keratin), and proteins too small to hold their shape on their own (eg. insulin).

Behaves similarly to glutamic acid. Carries a hydrophilic acidic group with strong negative charge. Usually is located on the outer surface of the protein, making it water-soluble. Binds to positively-charged molecules and ions, often used in enzymes to fix the metal ion. When located inside of the protein, aspartate and glutamate are usually paired with arginine and lysine.

Essential for humans. Phenylalanine, tyrosine, and tryptophan contain large rigid aromatic group on the side chain. These are the biggest amino acids. Like isoleucine, leucine and valine, these are hydrophobic and tend to orient towards the interior of the folded protein molecule.

Because of the two hydrogen atoms at the α carbon, glycine is not optically active. It is the tiniest amino acid, rotates easily, adds flexibility to the protein chain. It is able to fit into the tightest spaces, e.g., the triple helix of collagen. As too much flexibility is usually not desired, as a structural component it is less common than alanine.

In even slightly acidic conditions protonation of the nitrogen occurs, changing the properties of histidine and the polypeptide as a whole. It is used by many proteins as a regulatory mechanism, changing the conformation and behavior of the polypeptide in acidic regions such as the late endosome or lysosome, enforcing conformation change in enzymes. However only a few histidines are needed for this, so it is comparatively scarce.

Essential for humans. Isoleucine, leucine and valine have large aliphatic hydrophobic side chains. Their molecules are rigid, and their mutual hydrophobic interactions are important for the correct folding of proteins, as these chains tend to be located inside of the protein molecule.

Essential for humans. Behaves similarly to arginine. Contains a long flexible side-chain with a positively-charged end. The flexibility of the chain makes lysine and arginine suitable for binding to molecules with many negative charges on their surfaces. E.g., DNA-binding proteins have their active regions rich with arginine and lysine. The strong charge makes these two amino acids prone to be located on the outer hydrophilic surfaces of the proteins; when they are found inside, they are usually paired with a corresponding negatively-charged amino acid, e.g., aspartate or glutamate.

Essential for humans. Always the first amino acid to be incorporated into a protein; sometimes removed after translation. Like cysteine, contains sulfur, but with a methyl group instead of hydrogen. This methyl group can be activated, and is used in many reactions where a new carbon atom is being added to another molecule.

Contains an unusual ring to the N-end amine group, which forces the CO-NH amide sequence into a fixed conformation. Can disrupt protein folding structures like α helix or β sheet, forcing the desired kink in the protein chain. Common in collagen, where it undergoes a posttranslational modification to hydroxyproline. Uncommon elsewhere.

Serine and threonine have a short group ended with a hydroxyl group. Its hydrogen is easy to remove, so serine and threonine often act as hydrogen donors in enzymes. Both are very hydrophylic, therefore the outer regions of soluble proteins tend to be rich with them.

Depending on how polar the side chain, aminoacids can be hydrophilic or hydrophobic to various degree. This influences their interaction with other structures, both within the protein itself and within other proteins. The distribution of hydrophilic and hydrophobic aminoacids determines the tertiary structure of the protein, and their physical location on the outside structure of the proteins influences their quaternary structure. For example, soluble proteins have surfaces rich with polar aminoacids like serine and threonine, while integral membrane proteins tend to have outer ring of hydrophobic aminoacids that anchors them to the lipid bilayer, and proteins anchored to the membrane have a hydrophobic end that locks into the membrane. Similarly, proteins that have to bind to positive-charged molecules have surfaces rich with negatively charged aminoacids like glutamate and aspartate, while proteins binding to negative-charged molecules have surfaces rich with positively charged chains like lysine and arginine.